From VISTA LAB WIKI
The Matlab software interface we use for analyzing functional and anatomical data mrVista, is pronounced mister-Vista. The MR stands for magnetic resonance and the VISTA refers to the VISTALAB name (vision, image science, and technology applications) that the Wandell lab has used for more than 15 years.
Elsewhere in this manual you can find a primer on functional MRI.
 Functional-MR Page Jump
- Intro to mrVISTA
- Functional Sequences
- Initializing Data into mrVista Format
- Pre-Processing Functional Data
- Motion Correction
- Coherence and Statistics
- GLM analyses
- Event Related Experiments
- Visual Field Maps
- pRF Model page
- Exporting Data as NIFTIs
MrVista offers several ways to interact with functional and anatomical data.
- Inplane views represent the data in the format that comes out of the scanner, overlaying maps computed off the functional images onto coregistered anatomical images;
- Volume and Gray views represent the data as aligned to a reference volume. The difference between the views is that the Gray view restricts the data to the segmented gray matter surface. Gray and Volume views can have their data projected on to a 3D reconstruction of the gray matter surface, or 'Mesh', which is tied to this view.
- Flat views represent the gray matter-restricted data as projected on to a 2-dimensional ("flattened") cortical surface.
MrVista is also an interface to a range of analysis methods. These include
- General linear model (GLM) and event-related methods (Rory Sayres).
- Retinotopy (visual field maps) (Steve Engel)
- Population receptive fields (Serge Dumoulin).
- Flattening the cortical surface (Alex Wade) and
- Mesh (3D) visualization methods (Alex Wade, Bob Dougherty)
The MR pulse sequence and data pre-processing methods are described in separate pages. They include a review of the spiral pulse sequences, SSFP methods, and pre-processing of the functional data. They also describe the pre-processing of the data, which involves reconstructing the time series images (reconning) and transferring the data from the Lucas Center to our lab computers.
The functional data are integrated with the diffusion imaging using the mrDiffusion tools developed by Bob Dougherty. He built those tools and also played a significant role in developing most of the MrVista tools.
There is an older tutorial of the interface for the psych 204 class.
- Tutorial for mrVista, oriented towards KGS-lab processing conventions (On an Internal page for Grill-Spector/Wandell lab members).
(Minor footnote of interest to N < 10 people: Originally the Wandell and Heeger labs, including Engel, Boynton, Poirson, and others, developed the MR software together. After Dave Heeger went to the big Apple, his lab branched. Their Wiki page uses the classic name of the software, mrLoadRet. This was the name Steve Engel used, referring to magnetic resonance, load retinotopy data. Larsson, Schluppeck, Gardner, and others added to their tools. Whenever we visit, we say that we should merge things. I hope that happens some day.)
Spiral Pulse Sequences
- Glover GH, Lai S., 1998. Self-navigated spiral fMRI: interleaved versus single-shot. Magn Reson Med. 1998 Mar;39(3):361-8.
- Lai S, Glover GH., 1998. Three-dimensional spiral fMRI technique: a comparison with 2D spiral acquisition. Magn Reson Med. 1998 Jan;39(1):68-78.
- Nestares O, Heeger DJ., 2000 Robust multiresolution alignment of MRI brain volumes. Magn Reson Med. 2000 May;43(5):705-15.
Traveling Wave Analyses
- Engel SA, Rumelhart DE, Wandell BA, Lee AT, Glover GH, Chichilnisky EJ, Shadlen MN., 1994. fMRI of human visual cortex. Nature. 1994 Jun 16;369(6481):525. PubMed
General Linear Model
- Keith J. Worsley, Statistical Analysis of Activation Images (Chapter 14). In: Functional Magnetic Resonance Imaging: An Introduction to Methods (Eds. P. Jezzard, P.M. Matthews and S.M. Smith), Oxford University Press.
- Burock MA, Dale AM., 2000. Estimation and detection of event-related fMRI signals with temporally correlated noise: a statistically efficient and unbiased approach. Hum Brain Mapp. 2000 Dec;11(4):249-60. PubMed
- Free Surfer Formulation of event-related analyses
- White paper describing motivation behind BOLD event-related contrast
Much Older VISTA lab manual